Rise of the Samurai
by LloydandNyaLover101
Summary: When the boys die in battle, Nya, Garmadon, Misako and Sensei Wu are found by Commander Reed. After a year of training, Nya is ready for something unexpected. What will happen? Find out! No flames!
1. Chapter 1

**_SUP PEOPLES! WHAT UP?! So, I got this idea from watching the new movie Pacific Rim...I loved it...you should watch it. Anyway, after the movie, I decided to make this story._**

**_Kai: Great. You deleted the other stories, nice. _**

**_Me: SHUT UP KAI! YOU DIE BY THE WAY! _**

**_Kai Fangirls: NOOO!_**

**_Me: *Pushes them out* Anyway, the five boys die in the story, so sorry all you fangirls! _**

**_Cole: Why? I thought you loved me! _**

**_Jay: What about Nya? Will she die?_**

**_Me: No Jay, she'll be alive. She'll be the main character in this._**

**_Jay: WHAT?! *Starts rambling* _**

**_Me: *Slaps hand over mouth* Sorry, it'll be a year after the boys died. I won't reveal the plot. _**

**_Disclaimer: I do not own Ninjago, I only own the OC's and plot!_**

* * *

**_Chapter 1_** **  
**

Nya flipped Jason over her shoulder and onto the training mat. He got back up and and stood in a fighting stance. Nya took her staff out and so did Jason. Nya stood straight and made a signal to him saying 'Come on'. He ran after her and she blocked his blows with her staff. She got his staff and threw it along with her's. Jason threw punches at her but she blocked them. She flipped over him and took him out. She held her staff to his neck.

''Very good Nya!'' Wu says

''Thank you, Sensei.'' Nya says. She holds her hand to him and he takes it gratefully.

''Nice match.'' Jason says

''Thanks. You know you gotta be quicker then that if you ever want to beat me.'' Nya says

''Ha, I let you win.'' Jason replied

''Yeah right.'' Nya says rolling her eyes knowing the real reason. They walked to the cafeteria and Sensei Wu and Commander Reed were talking.

''She is amazing. I think she's ready to be-'' Reed started

''Shh, keep quiet! Do you want to spoil it to me?'' Wu cut in

''Sorry, tomorrow I'll announce it.'' Reed says bowing to Wu

''Great.''

* * *

Nya took her red hair tie out and ran her hair threw her longer hair. Her hair went to her middle back now and streaks of different colors ran threw it. Her bangs fell in her eyes. She groaned. She brushed her hair, then put it in a braid. A knock on the door was heard, and Misako slipped in.

''Hey Misako.'' Nya whispered

''Hey Nya. You were great out there.'' Misako says sitting on her bed. Nya sat by her.

''Thanks.'' Nya replied

''You know, I was looking in some scrolls, and five more girls who are ninja.'' Misako says trying to cheer Nya up. It didn't work.

''More Ninja?'' Nya asks tears welling up in her eyes

''Yeah.'' Nya broke down crying. Misako brought her close and rubbed her back. Garmadon opened the door and walked in, closing the door behind him.

''Everything okay?'' He asks sitting down beside Nya

''No, I just told her about a prophecy about five more ninja, and she broke down crying. I think she's still upset about what happened a year ago.'' Misako says

''They died Ninja at least.'' Garmadon says kissing her cheek. Nya was asleep and curled up in a ball.

''Should we go or stay?'' Misako whispered

''Stay.'' Garmadon replies caressing Nya's cheek. Misako and Garmadon kissed then fell asleep.

* * *

Nya's eyes fluttered open. She noticed herself curled up between Garmadon and Misako. She screamed and fell off the bed, waking the grown ups in the process.

''Nya?''

''I'm OK.'' She says getting up and brushing herself off. The intercom came on.

''All students in training and other's come to the cafeteria.'' They looked at each other and shrugged. When they got there, Nya walked to her friends.

''What's going on?'' She asks

''Commander Reed is going to announce his new second in command.'' Jason informed

''Really? What happened to his last one?''

''Died in battle against the Nindroids.'' Her friend Harmony replied. _'Just like my family.' _She thought sadly. Reed came onto the stage.

''I am pleased with the progress the students have been making, thanks to Sensei Wu. I will choose one of you to become my new second in command. My last died in battle and now I have to pick one.''

''Wonder who, it can't be Tyson.'' Her other friend Skyla says. Tyson was a strong, well built man who was stronger then Cole...maybe. Nya saw him and he winked at her. She growled under her breath.

''Now, my new second in command is, Nya Smith!'' He announced. Nya's jaw dropped and her eyes went wide. Her friends hugged her and she walked on stage. Reed took her hand and put in the air. Misako and Garmadon hugged her and Wu smiled and winked at her. Unfortunately, the happy moment didn't last long. Skyla and the other's ran to the computer room and she pulled a picture up of General Cryptor and 15 other Nindroids at a village.

''They're attacking Igancia Village!''

''My home!'' Nya gasped. She ran to her room where a box laid with a symbol of Fire and Lightning was engraved. She smirked.

This was going to be awesome.

* * *

**Cliffy! Little GarmadonxMisako fluff! So, yes the boys died during a battle against the Nindroids. **

**Kai and Cole: I thought you loved me! **

**Me: I do! But there aren't many stories of Nya. Sorry boys. **

**Nya: Plz review!**


	2. Chapter 2

_**Hey! I'm back for more tortur- I mean writing!**_

_**Jason: YAY! I GET TO SEE NYA! **_

_**Jay: *Growls and tackles him* She's mine! **_

_**Me: Get off him! *Pulls him from Jason* Jay, he meant they were apart for a night, and they have hung out ever since they meant!**_

_**Jay: Oh.**_

_**Nya: Can we get on with the story now? **_

_**Me: Yes.**_

_**Disclaimer: I don't own Ninjago, lego does, I only own the OC's and the plot. **_

* * *

**_Chapter 2 _**

Nya ran to the front of the base and saw Reed with 24 other troopers. Jason's eyes widened at the sight of her. Her middle back black hair was in a bun now instead if her braid, her uniform was black, red and gold armor with black boots, two katanas were on her back and two daggers were held by a black belt. Jason was staring at her muttering 'beautiful' over and over again.

''Nya, you will lead them into battle. Boys, listen to her.'' Reed commanded and they nodded. They ran to the village and hid behind some rocks. General Cryptor and 10 Nindroids stood around Four weapons. Nya growled.

''What's the plan?'' A solider asked her. She turned to them.

''Jason follow me, when I wink, you guys come out. OK?'' They nodded. Nya jumped into a tree with Jason following. A clearing in the tree was shown and they peaked out. Nya looked at Jason and smiled. She jumped onto the roof. The Nindroids looked at her.

''Attack her you fools!'' Cryptor shouted. She winked and the army came out.

''NYA!'' Jason yelled. A Nindroid stood over him with a sharp sword.

''JASON!'' She ran and took it out. She offered a hand to him and he took it.

''RETREAT!'' Cryptor screamed. Only five left with him. When they got back to the base, Nya was showered with 'You did it' and so on.

''You guys are alive!'' Skyla says hugging Nya and Jason. Harmony did too.

''Of course we are!'' Jason replied. Garmadon and Misako sneaked up behind Nya and Garmadon hugged her from behind.

''You were amazing out there!'' Misako says. Nya blushes from embarrassment.

''Garmadon! I'm in front of my friends!'' Nya muttered

''You're starting to sound like Lloyd!'' Nya's face saddened at her companions' name.

''Sorry. I'm so proud of you.'' Misako says her eyes misty. She and Nya hug.

''I'm going to go change.'' Nya whispers. She walks to her room and opens her door. Her royal blue room shined in the moonlight, her red bedspread had Japanese designs, her mirror and desk was neat and her dresser stood against a wall. A bookshelf that had a few books and pictures stood against the wall also. A nightstand had a picture of her and her friends on it. She took her armor off leaving her suit on. She walked to her bathroom and took a shower. Laughs of her family still rung in her mind. Images of them made a tear fall down her face. She turned the water off and wrapped a towel around her body. She got her black clothes and put her hair in the normal braid.

Nya walked up to the roof and she sat on the edge. The falcon perched next to her. She rubbed it's head. A groan of pain caught her attention from the trees. She jumped off and landed perfectly on the ground. She walked to the trees, and pushed the bushes away. She gasped once she saw the sight. Laying there was a boy with blonde hair. He had cuts on his face, gashes on his arms and forehead and bruises on his body. His kimono was torn also. She ran to him and turned him over revealing his half opened eyes. She could make the color out. And immediately knew who it was.

''Zane..''

* * *

**_AHHHHHHHHH! ZANE'S ALIVE! Well, half alive. Can Nya get him to the base in time before he dies? Please review!_**


	3. Chapter 3

**_I'M BACK! *Evil laugh* _**

**_Ninja and Nya: *In a corner shaking with fear* _**

**_Me: Don't worry, goodness. It's like I'm living with a bunch of five year olds._**

**_Jason, Skyla, Harmony, and Dana: *Snickers* _**

**_Me: Anyway, here's chapter 3! _**

**_Disclaimer: I do not own NINJAGO, LEGO does!_**

* * *

**_Chapter 3_**

Nya breathed heavily and pushed his bangs back. She looked up at the falcon then back at Zane. She got up and ran back to the base to get help. She burst threw the training doors where all of the boys and girls were training. Their eyes turned to her. Sensei Wu's eyebrow cocked. She walked calmly to him and whispered in his ear. Harmony, Skyla, Dana and Jason shrugged to each other. Sensei's eyes widened.

''Dana, Skyla, Jason and Harmony, come with me.'' Nya says walking passed them. They looked at each other and followed her to the trees.

* * *

''How did he end up like this?'' Skyla asks observing him. His breathing was light and his eyes were closed.

''I don't know. I heard him groan in pain and I found him like this. It was probably the Nindroids.'' Nya explained

''We should probably get him to the Infirmary.'' Dana suggested. They nodded and picked him up. They got him to the Infirmary and Nya cleansed his wounds. When she got to his face, a ton of dirt and blood was washed off. His pale skin was visible again, his pale blonde hair which was covered in blood was washed, and his kimono was changed. He laid on the bed, motionless. They sat around the fire with hot chocolate. Nya's eyes were closed and tears peaked out on the ends. They fell down her face.

''Nya? Are you alright?'' Harmony asks concerned for her friend. Nya looked up.

''Yeah. I'm just worried.'' She replied wiping them away. A groan from Zane made her stand up and walk to him. His eyes started opening and saw Nya's gentle gray eyes. They were pricked with tears.

''N-Nya?'' He whispered

''Hey Zane.'' Nya whispered brushing his hair away. He tried to sit up, but Nya pushed him back down.

''Nya, let me sit up.'' He says. Her eyes were hard.

''No. I don't want you to get hurt anymore.'' She replied. He was shocked that she said that.

''But..''

''No. I can't let you.'' She whispers. She turns around and whispers something to Dana. She nods. Nya opened the door, but before she walked out, she turned her head to Zane.

''Goodnight Zane.'' She slams the door making them jump.

* * *

Misako was in the library when she heard some crying. She walked out and walked to Nya's dorm. She knocked. No answer. She opened the door and saw Nya crying on the bed. Her eyes softened and walked to her. She sat by her and stroked her hair that came out of her braid.

''Misako?''

''Yes Nya?''

''You know how the boys died?''

''Yes.''

''Well, Zane survived and I found him beat up in the forest. We brought him here and he woke up.'' Nya explained. Misako's eyes were wide and glistened with tears.

''Oh.''

''I didn't know what to do.'' Nya says more tears pouring. Misako brought her head to her lap and rubbed her back. Nya sat up.

''You should tell him how you feel.'' Misako says wiping her tears away. She nodded and got up. Her hand rested on the knob. She turned around and ran to Misako. She hugged her and smiled.

''Thank you.'' She says. Nya pulled away and went back to the Infirmary.

* * *

''Sir, I'm afraid he got away.'' A Nindroid says

''Which one?''

''The Nindroid.'' Cryptor growled. The Nindroid stood in front of him calmly.

''He was beat up though. He'll never make it alive.'' He explained. General Cryptor smirked evilly.

''I knew I could count on you. Even if we win, the army will fall for them.'' He laughed.

''What do you want me to do?'' He asks

''I want you to kill the second in command, or bring her here, alive.'' He says. The Nindroid bowed and walked away. Cryptor smiled and waved his hand. A wall opened and a dungeon was revealed.

''You aren't getting her!'' A boy screamed

''Foolish boy. Don't you see, she's forgotten about you.'' The boys' eyes saddened. A ball came up. It showed Nya and her friends.

''She made new friends and became second in command.'' Another boy came up and his mouth was dropped. The ball changed it's scene and showed her training. Two more boys came and had their mouths dropped. The ball then disappeared and Cryptor walked to the cage. He typed in a code and the wall closed.

''Pity that you had to say goodbye.'' He says smirking. He sat on his throne again.

* * *

''Nya, he's asleep.'' Jason says to Nya

''Really?'' He nodded. Nya walked to Zane's bed and saw him asleep. She pushed his bangs back and walked out.

''Are you sure they're not playing with us?''

''What do you mean?''

''I mean, what if he's a clone from the Nindroids?''

''He isn't, Jason.'' Nya replied

''Oh, night.'' He says then walks to his dorm. Nya opened her door and laid on the bed. She rolled over and saw the photo of her and the others' after the defeat of the Overlord. A tear fell from her eye. She closed her eyes and fell asleep.

* * *

_**YAY! ZANE'S FULLY ALIVE!**_

_**Zane: *Smiles* **_

_**Me: Who were the boys? Find out later! **_

_**Nya: Please review!**_


	4. Chapter 4

**_ANOTHER CHAPTER! YAY! _**

**_Jason: Took you long enough!_**

**_Me: I was busy! _**

**_Harmony: Kai, can I talk to you? _**

**_Kai: Sure. *Goes to other room* _**

**_Me: What do you think their talking about? *Hears a gasp and thud* _**

**_Nya: We'll check on them later! _**

**_Disclaimer: I do not own NINJAGO, LEGO does! _**

* * *

_**Chapter 4**_

Nya woke up to the siren and jumped out of bed. She ran to the the Computer room to find the others there. She pushed threw the crowd and saw the General Cryptor on screen.

''_There you are Second in Command!_'' He says. She growled.

''What do you want?'' She asks darkly

''_Nothing really, but I'll make a deal with you. You tell me where your base is or you can perish just like your family._'' He says

''No! I will never tell you! You have caused too much sorrow and I will never tell you! You killed my family, they were the only one's I had left until you had to come in and kill them! They were awesome Ninja and I don't care if I was a ninja or not, you will never find us!'' Nya screamed tears streaming down her cheeks. Everyone stared at her wide eyed. The picture disappeared, and Nya looked down.

''I'm sorry Kai.'' She muttered. She ran out with her friends following her. Misako was about to go, but was held back by Garmadon.

* * *

Nya was sitting on the edge of the roof. Her friends sat by her. She stopped crying.

''I still don't get why Cryptor wants to get our base.'' Jason says pacing

''Yeah, why though?'' Harmony asks

''Because he knows I was the Samurai.'' They look at her.

''What do you mean?'' Skyla asks

''I was the sister of Kai, Ninja of Fire. He knows that I'm Samurai X.'' Nya replies

''Your brother was a Ninja?'' Dana asks. She nods.

''He and the others defeated so many evils. Zane, Ninja of Ice, Cole, Ninja of Earth, Jay, Ninja of Lightning, and Lloyd, Green Ninja, Master of all Elements. They were my friends. My family. But I failed to protect them.'' She says. They hug her. Misako ran up.

''Zane's awake.'' She says. Nya gasps and runs to the Infirmary.

* * *

Zane was sitting up reading when Nya came in. He looked up and saw her. He smiled.

''Zane!'' She squeals. Nya runs to him and hugs him.

''Nya!'' He says hugging her back. A cleared throat was heard. Nya turned around.

''Commander Reed! What are you doing here?'' She asks. Zane looked at her braid and his eyes went wide.

''Misako got me. She wants to tell you something.'' Reed responded. Misako came in with a golden scroll. Jason, Skyla, Harmony, Dana, Nya and Zane stood around the table. Well, Zane sat.

''You six have to find the six Elements of Legend.''

''The six Elements of what now?!''

* * *

**_Chapter 5 is done! YAY! Nya, did you find out what's wrong? _**

**_Nya: Yeah, I'm gonna be a aunt. _**

**_Me and the others: WHAT?! _**

**_Me: Tune in for the next chapter! PLEASE REVIEW!_**


	5. Chapter 5

_**I'M BACK! **_

_**Ninja: :) **_

_**Me: Kai, Harmony, congratulations. **_

_**Them: Thanks! **_

_**Disclaimer: I do not NINJAGO, LEGO does! **_

* * *

_**Chapter 5**_

The six stared at her.

''What are they exactly?'' Nya asks

''The Elements of Legend are very rare to be heard, but they are known to be in the Castle of Light.''

''Castle of Light?'' Skyla asks

''Yes. The First Spinjitzu Master lived there along with his wife.'' Misako says

''Wait, I thought they lived in the Monastery.'' Nya says

''They built it after they died. The castle disappeared with no trace. That is all I know. The Six Elements of Legend disappeared along with it.''

''What are the elements?'' Zane asks

''Wind, Sound, Ice, Metal, and Nature. The sixth is a complete mystery.'' Misako replies

''Those are really weird elements.'' Jason says only to get punched in the arm by Skyla. Misako smiled.

''They are, you have to start searching for them right away, or we'll be living under a dark cloud forever.''

''We'll leave right away.'' Nya says helping Zane up. Misako nodded.

''Pack the things you'll need.'' Reed says. They nod.

* * *

''I can't wait for this trip.'' Skyla says sitting on Nya's bed. Zane, Jason, Harmony, Skyla, Dana, and Nya just finished packing and were hanging out for a minute. Dr. Julien came in and gave them a earpiece.

''When you are in trouble, talk into these.'' He says

''Thank you. Come on guys, let's find those Elements of Legend!'' Nya says. They run to the front and find them talking. Nya walked to them with the others following.

''Nya, the Castle of Light is in the middle of Ninjago. It's a three day trip. May we come?'' Misako pleaded

''Sure.'' She says

* * *

Once they were in the forest, there was a long silence. As they were walking, Harmony was humming, Zane was thinking, Jason looked around, Dana was expecting everything, Skyla was walking closely to Zane, Misako was looking at a scroll, Garmadon was silent, and Nya was leading. A few hours later, the sun started setting.

''We should set up camp.'' Nya suggested. They nodded.

''I'll gather some firewood.'' Jason says. After they had a fire going and everything was peaceful, well, until a twig snapped. They peaked out of the bushes and saw a hooded figure. It was by a bush filled with pink flowers. She picked two and put them in a little bag. It looked at the bush where they were, and they quickly hid. They peaked out again, and it was gone.

''What are you doing out in these woods?'' A female voice asks making them whip around. The hooded figure was there. Nya stood up followed by the others.

''Um, we came to find the Castle of Light.'' She says. The figure gasps and reveals herself. She had light brown hair that went to her neck and pale blue eyes.

''Come, you must not be seen!'' She says. They get their stuff and run after the girl. She led them to a little hut not far from their campsite.

''Uh, why did you bring us here?'' Garmadon asks

''There are more secrets to the Castle then you know. I am Zora, by the way.'' Zora says. They walk inside and Zora closes the blinds leaving a little candle on.

''So, what are the secrets?'' Jason asks. Zora smiles softly and brings a bejeweled bottle with a white liquid inside.

''This will help you see the past, Nya.'' Nya looked at the others.

''Are you sure it won't kill me?'' She asks

''I'm sure it won't kill you.'' Zora says. Nya takes it and looks at her. She nods. She sips a little.

''I don't think it's -!'' Her eyes went white.

**_(Flashback, 14 years ago) _**

_A young girl about three was running in a gold dress. She had ebony hair, amber eyes and a little tiara on her head. _

_''You can't catch me mommy!'' She yelled. Misako appeared in a green dress with her hair down and a golden crown was on her head also. She was running after the little girl that was her daughter. _

_''Nya! Come here!'' Misako laughed. Nya was caught by her mother. They laughed. Misako brought her to the throne room where Garmadon and Wu were. _

_''Uncle! You're here!'' Nya squeals and jumps out of Misako's arms and runs to Wu. _

_''Hey cutie!'' Wu chuckles hugging her_

_''Did you bring it?'' Wu brings a book out and she takes it from him. _

_''Yay! Thank you Uncle!'' She runs to her father and sits down. _

_''Thank you Wu.'' Garmadon thanks his brother. He nods. _

_''I must go now. I got to clean the library again.'' He says_

_''Bye Wu!'' Before he could exit, a dark shadow loomed over the castle. Nya squeaked and ran behind her mother with her book. Garmadon and Wu stood next to each other. _

_''Misako, get Nya out of here!'' Wu yelled. Misako picked up the frightened child and ran. Her dress tore and she found a little weaponry. She put Nya to sleep with a lullaby. She then found a basket perfect for her. She set her in it and kissed her forehead. _

_''I love you.'' She put her book next to her and knocked. She ran and looked back. The door opened and saw the mother. She gasped and picked Nya up and her book. Misako disappeared. _

**_(End of Flashback)_ **

Nya shook her head and rubbed her eyes. The others were looking at her.

''Why are you all looking at me like that?'' She asks

''It's just, you were mumbling to yourself.'' Harmony says

''Oh! Don't forget the constant sobbing!'' Jason added

''Did you see anything?'' Dana asks

''Well, I did see the Overlord and the Castle of Light.'' She says

''Maybe another sip will help.'' Zora says. Nya drank one more sip and her eyes turned white again.

* * *

_**What do you think Nya will see in this flashback? Nya, how's Harmony?**_

_**Nya: OK, but she just, how do I put this, um, went into labor. **_

_**Me: Oh. Please review!**_


End file.
